They said the bomb was placed on the tracks and exploded when the train passed over it as it was passing a station in Pattani province.
The blast blew the last carriage of the train tracks. The train was on its way from Sungai Golak to Hatyai, near the border with Malaysia.
Southern Thailand, which has a majority Muslim population in a predominantly Buddhist country, has for years been in the grip of a separatist insurgency.
The insurgents regularly carry out bombings and assassinations against government targets.
S/SH 11